Additional File 4: Biological Processes

Additional file 4: FOS affected colonic genes/ Biological processes Rodenburg et al

Additional file 4: Biological processes

Genes affected by FOS and part of a significantly regulated biological process.

Genes included in this selection have a p-values<0.001 or are selected by RF.

Biological process / Gene name / Gene symbol / Sequence ID / Fold change / P-value
Mitochondria
Complex I
NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 6 / Ndufb6 / XM_216378 / 1.54 / <0.001
NADH dehydrogenase (ubiquinone) Fe-S protein 5b, 15kDa (NADH-coenzyme Q reductase) / Ndufs5a / XM_227473 / 1.54 / <0.001
NADH dehydrogenase (ubiquinone) Fe-S protein 6 / Ndufs6 / NM_019223 / 1.48 / <0.001
NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 9 / Ndufb9 / XM_216929 / 1.47 / <0.001
NADH dehydrogenase (ubiquinone) flavoprotein 2 / Ndufv2 / NM_031064 / 1.47 / <0.001
NADH-ubiquinone oxidoreductase B9 subunit (Complex I-B9) (CI-B9) / Ndufa3 / XM_341773 / 1.46 / <0.001
NADH dehydrogenase (ubiquinone) 1 beta subcomplex 3 / Ndufb3 / XM_344609 / 1.46 / <0.001
NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 2 / Ndufa2 / XM_214570 / 1.46 / <0.001
NADH dehydrogenase (ubiquinone) Fe-S protein 8 / Ndufs8 / XM_215197 / 1.45 / <0.001
NADH dehydrogenase (ubiquinone) 1 beta subcomplex 8 / Ndufb8 / XM_215269 / 1.45 / <0.001
NADH dehydrogenase (ubiquinone) flavoprotein 3-like / Nduf3 / NM_022607 / 1.44 / <0.001
NADH-ubiquinone oxidoreductase PDSW subunit (Complex I-PDSW) / Ndufb10 / XM_213242 / 1.42 / <0.001
NADH dehydrogenase (ubiquinone) 1NADH dehydrogenase (ubiquinone) 1alpha subcomplex, 13 / Ndufa13 / XR_008769 / 1.41 / 0.001
NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 7 / Ndufb7 / XM_341664 / 1.40 / 0.001
NADH dehydrogenase (ubiquinone) 1, alpha/beta subcomplex, 1 / Ndufab1 / XM_215044 / 1.38 / <0.001
NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 12 / Ndufa12 / XM_216880 / 1.38 / <0.001
NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 11 / Ndufb11 / XM_216785 / 1.37 / <0.001
NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 4 / Ndufa4 / NM_010886 / 1.36 / <0.001
NADH dehydrogenase (ubiquinone) 1 beta subcomplex, 5 / Ndufb5 / XM_215544 / 1.34 / <0.001
NADH dehydrogenase (ubiquinone) 1 alpha subcomplex 11 / Ndufa11 / NM_212517 / 1.33 / <0.001
NADH dehydrogenase (ubiquinone) 1, subcomplex unknown, 2 / Ndufc2 / NM_001009290 / 1.32 / <0.001
NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 8 / Ndufa8 / XM_216044 / 1.32 / <0.001
NADH dehydrogenase 1 alpha subcomplex 10-like protein / Ndufa10l / NM_182671 / 1.30 / <0.001
NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 7 (B14.5a) / Ndufa7 / XM_216859 / 1.28 / 0.002
glycerol-3-phosphate dehydrogenase 2, mitochondrial / Gpd2 / NM_012736 / 1.27 / 0.001
NADH dehydrogenase (ubiquinone) Fe-S protein 3 / Ndufs3 / XM_215776 / 1.26 / <0.001
NADH dehydrogenase (ubiquinone) flavoprotein 1 / Ndufv1 / NM_001006972 / 1.24 / <0.001
Complex II
electron-transferring-flavoprotein dehydrogenase / Etfdh / NM_198742 / 1.51 / <0.001
succinate dehydrogenase complex, subunit B, iron sulfur (Ip) / Sdhb / XM_216558 / 1.43 / <0.001
succinate-CoA ligase, GDP-forming, alpha subunit / Suclg1 / NM_053752 / 1.36 / <0.001
Succinate dehydrogenase A / Sdha / XM_215279 / 1.35 / <0.001
succinate dehydrogenase complex, subunit C, integral membrane protein / Sdhc / NM_001005534 / 1.31 / <0.001
Complex III
ubiquinol-cytochrome c reductase binding protein / Uqcrb / XM_224385 / 1.53 / <0.001
ubiquinol-cytochrome c reductase hinge protein / Uqcrh / NM_001009480 / 1.39 / <0.001
ubiquinol-cytochrome c reductase complex 7.2kDa protein isoform a / Uqcrc / BF556101 / 1.36 / <0.001
Complex IV
cytochrome c oxidase subunit VIIb / Cox7b / NM_182819 / 1.61 / <0.001
cytochrome c oxidase, subunit VIc / Cox6c / NM_019360 / 1.54 / <0.001
cytochrome c oxidase subunit Vb / Cox5b / NM_053586 / 1.51 / <0.001
cytochrome c oxidase, subunit VIIa 2 / Cox7a3 / NM_022503 / 1.50 / <0.001
cytochrome c oxidase subunit VIIa-L precursor / LOC365879 / XM_345256 / 1.50 / <0.001
cytochrome c oxidase subunit VIc-1 / COX-VIc-1 / NM_173303 / 1.50 / <0.001
cytochrome c oxidase, subunit VIa, polypeptide 1 / Cox6a1 / XM_341094 / 1.48 / <0.001
Cytochrome c, somatic / Cytc / XM_218990 / 1.34 / 0.001
cytochrome c oxidase, subunit Va / Cox5a / NM_145783 / 1.30 / <0.001
cytochrome c oxidase, subunit VIIIa / Cox8a / L48209 / 1.29 / <0.001
SCO cytochrome oxidase deficient homolog 1 (yeast) / XM_573117 / 1.28 / 0.001
COX10 homolog, cytochrome c oxidase assembly protein, heme A: farnesyltransferase / Cox10 / TC475388 / 1.24 / <0.001
COX4 neighbor / Cox4 / XM_341703 / 1.20 / 0.002
Complex V
ATPase inhibitory factor 1 / Atpi / NM_012915 / 1.59 / <0.001
ATPase inhibitory factor 1 / If1 / TC512274 / 1.54 / <0.001
ATP synthase, H+ transporting, mitochondrial F0 complex, subunit f, isoform 2 / Atpf2 / BM986304 / 1.52 / <0.001
ATP synthase, H+ transporting, mitochondrial F0 complex, subunit G / Atp5g / XM_345982 / 1.52 / <0.001
ATP synthase, H+ transporting, mitochondrial F0 complex, subunit e / Atp5i / NM_080481 / 1.49 / <0.001
ATP synthase D chain, mitochondrial / Atpd / XM_224879 / 1.48 / <0.001
ATP synthase, H+ transporting, mitochondrial F0 complex, subunit d / Atp5h / NM_019383 / 1.46 / <0.001
ATP synthase, H+ transporting, mitochondrial F0 complex, subunit F6 / Atp5j / NM_053602 / 1.43 / <0.001
ATP synthase, H+ transporting, mitochondrial F0 complex, subunit b, isoform 1 / Atp5f1 / NM_134365 / 1.37 / <0.001
ATP synthase, H+ transporting, mitochondrial F1 complex, O subunit / Atp5o / NM_138883 / 1.36 / <0.001
ATP synthase lipid-binding protein, mitochondrial precursor (ATP synthase proteolipid P1) / Atpc / XM_222276 / 1.32 / <0.001
ATP binding domain 3 / Atpb3 / XM_218640 / 1.30 / <0.001
ATP-binding cassette, sub-family G (WHITE), member 4 / Abcg4 / XM_236186 / 1.29 / <0.001
ATP synthase, H+ transporting, mitochondrial F1 complex, delta subunit / Atp5d / NM_139106 / 1.28 / <0.001
ATP synthase, H+ transporting, mitochondrial F0 complex, subunit c (subunit 9), isoform 1 / Atp5g1 / NM_017311 / 1.25 / <0.001
ATPase, H transporting, lysosomal V1 subunit G1 / Atpv1g / XM_216411 / 1.25 / <0.001
ATP-binding cassette, sub-family A (ABC1), member 2 / Abca2 / NM_024396 / 1.25 / 0.007
ATP synthase, H+ transporting, mitochondrial F0 complex, subunit c (subunit 9), isoform 2 / Atp5g2 / NM_133556 / 1.21 / <0.001
ATPase, H+ transporting, V1 subunit A, isoform 1 / Atpv1 / TC465908 / 1.17 / 0.001
ATPase, Na+/K+ transporting, beta 1 polypeptide / Atp1b1 / NM_013113 / 1.16 / 0.001
ATP-binding cassette, sub-family A (ABC1), member 1 / Abca1 / NM_178095 / 1.15 / 0.009
Metabolism and TCA cycle
aldo-keto reductase family 1, member B8 / Akr1b8 / NM_173136 / 2.13 / <0.001
aldo-keto reductase family 1, member C12 / Akr1c12 / XM_341549 / 1.88 / <0.001
3-hydroxybutyrate dehydrogenase (heart, mitochondrial) / Bdh / AW918701 / 1.85 / <0.001
quinolinate phosphoribosyltransferase / Qprt / NM_001009646 / 1.82 / <0.001
diazepam binding inhibitor / Dbi / NM_031853 / 1.68 / <0.001
pseudogene for diazepam binding inhibitor 1 / Dbii1 / XM_237195 / 1.67 / <0.001
malic enzyme 1 / Me1 / M30596 / 1.65 / <0.001
aldehyde dehydrogenase 2 / Aldh2 / NM_032416 / 1.63 / <0.001
acetyl-Coenzyme A acyltransferase 2 (mitochondrial 3-oxoacyl-Coenzyme A thiolase) / Acaa2 / NM_130433 / 1.56 / <0.001
Propionyl-CoA carboxylase alpha chain, mitochondrial precursor (PCCase alpha subunit) / Pcca / XM_341383 / 1.48 / <0.001
creatine kinase, brain / Ckb / NM_012529 / 1.48 / <0.001
demethyl-Q 7 / Coq7 / NM_012785 / 1.44 / <0.001
acyl-Coenzyme A dehydrogenase, very long chain / Acadvl / NM_012891 / 1.43 / <0.001
hydroxyacyl-Coenzyme A dehydrogenase type II / Hsd17b10 / NM_031682 / 1.41 / <0.001
sterol carrier protein 2 / Scp2 / NM_138508 / 1.39 / <0.001
malic enzyme 2, NAD(+)-dependent, mitochondrial / Me2 / XM_225729 / 1.38 / <0.001
3-hydroxy-3-methylglutaryl-Coenzyme A synthase 1 / Hmgcs1 / NM_017268 / 1.38 / 0.008
lactamase, beta 2 / Lactb2 / XM_216316 / 1.38 / <0.001
malate dehydrogenase 1, NAD (soluble) / Mdh1 / NM_033235 / 1.38 / 0.002
glyceraldehyde-3-phosphate dehydrogenase / Gapdh / XM_233263 / 1.36 / <0.001
enoyl Coenzyme A hydratase domain containing 1 / Echdc1 / NM_001007734 / 1.35 / <0.001
fructose-1,6- biphosphatase 1 / Fbp1 / NM_012558 / 1.35 / 0.001
hydroxyacyl-Coenzyme A dehydrogenase/3-ketoacyl-Coenzyme A thiolase/ alpha subunit / Hadha / NM_130826 / 1.35 / <0.001
fumarate hydratase 1 / Fh1 / NM_017005 / 1.35 / <0.001
degenerative spermatocyte homolog 2 (Drosophila), lipid desaturase / Degs2 / XM_234532 / 1.34 / <0.001
nudix (nucleoside diphosphate linked moiety X)-type motif 19 / Nudt19 / NM_001004258 / 1.34 / <0.001
acyl-CoA synthetase short-chain family member 1 / Acas2l / XM_215897 / 1.32 / <0.001
isocitrate dehydrogenase 3 (NAD+) beta / Idh3B / NM_053581 / 1.32 / <0.001
mitochondrial acyl-CoA thioesterase 1 / Mte1 / NM_138907 / 1.32 / <0.001
aldo-keto reductase family 1, member B4 (aldose reductase) / Aldr1 / NM_012498 / 1.31 / 0.001
gamma-glutamyl hydrolase / Ggh / NM_012960 / 1.31 / 0.001
dihydrolipoamide S-succinyltransferase (E2 component of 2-oxo-glutarate complex) / Dlst / NM_001006981 / 1.31 / <0.001
Fumarate hydratase, mitochondrial precursor (Fumarase) / Fh / XR_008238 / 1.30 / <0.001
acetyl-coenzyme A carboxylase alpha / Acaca / X53003 / 1.30 / <0.001
glutaredoxin 5 homolog (S. cerevisiae) / Glrx5 / XM_343103 / 1.30 / <0.001
aldo-keto reductase family 1, member E1 / Akr1e1 / NM_001008342 / 1.30 / 0.001
glutaredoxin 2 (thioltransferase) / Glrx2 / XM_213890 / 1.28 / 0.002
fumarate hydratase 1 / Fh1 / NM_017005 / 1.27 / <0.001
solute carrier family 25 (mitochondrial carrier; adenine nucleotide translocator), member 3 / ANT / NM_139100 / 1.26 / <0.001
ACN9 homolog (S. cerevisiae) / Acn9 / XM_342641 / 1.25 / <0.001
dihydrolipoamide dehydrogenase / Dld / NM_199385 / 1.24 / <0.001
carbonic anhydrase 5a, mitochondrial / Ca5a / NM_019293 / 1.24 / <0.001
Aldose reductase (AR) (Aldehyde reductase) / Ar / XM_226245 / 1.23 / 0.001
Nonspecific lipid-transfer protein, mitochondrial precursor / Nsldp / XM_345499 / 1.23 / <0.001
enoyl Coenzyme A hydratase, short chain, 1, mitochondrial / Echs1 / NM_078623 / 1.23 / 0.001
exocyst complex component 3 / Exoc3 / XM_341745 / 1.23 / 0.001
retinoblastoma binding protein 6 / Rbbp6 / XM_219296 / 1.22 / <0.001
pyruvate dehydrogenase kinase, isoenzyme 3 / Pdk3 / LOC363473 / 1.22 / 0.001
3-hydroxy-3-methylglutaryl-Coenzyme A lyase / Hmgcl / NM_024386 / 1.18 / 0.001
diacylglycerol O-acyltransferase 1 / Dgat1 / NM_053437 / 1.15 / 0.001
novel Acyl Transferase C. elegans C50D2.7 (variant 1) / At1 / XM_235527 / 1.13 / 0.010
glucose phosphate isomerase / Gpi / BQ193604 / -1.28 / <0.001
3-oxoacid CoA transferase 2A / Oxct2a / XM_233493 / -1.23 / 0.001
adenosine monophosphate deaminase 2 (isoform L) / Ampd2 / XM_342313 / -1.20 / 0.008
Mitochondrial ribosomes
mitochondrial ribosomal protein S16 / Mrps16 / XM_214132 / 1.43 / <0.001
mitochondrial ribosomal protein L22 / Mrpl22 / XM_213307 / 1.42 / <0.001
mitochondrial ribosomal protein L41 / Mrpl41 / XM_216010 / 1.39 / <0.001
mitochondrial ribosomal protein L40 / Mrpl40 / XM_213588 / 1.38 / <0.001
mitochondrial ribosomal protein L13 / Mrpl13 / XM_236903 / 1.38 / <0.001
mitochondrial ribosomal protein S36 / Mrps36 / XM_215468 / 1.37 / <0.001
mitochondrial ribosomal protein S25 / Mrps25 / XM_216222 / 1.37 / <0.001
mitochondrial ribosomal protein L35 / Mrpl35 / XM_216169 / 1.37 / <0.001
ribosomal protein, mitochondrial, L12 / Mrpl12 / XM_221202 / 1.35 / <0.001
mitochondrial ribosomal protein L11 / mrpl11 / NM_001006973 / 1.34 / <0.001
mitochondrial ribosomal protein L42 isoform b / Mrlp42b / XM_213981 / 1.33 / 0.001
mitochondrial ribosomal protein L42 / Mrpl42 / XM_216882 / 1.33 / 0.001
mitochondrial ribosomal protein L24 / mrpl24 / NM_001007637 / 1.33 / <0.001
mitochondrial ribosomal protein L47 / Mrpl47 / XM_215546 / 1.32 / <0.001
mitochondrial ribosomal protein S14 / Mrps14 / XM_213906 / 1.32 / <0.001
mitochondrial ribosomal protein L20 / Mrpl20 / XM_216599 / 1.32 / <0.001
mitochondrial ribosomal protein S15 / Mrps15 / NM_001007653 / 1.30 / <0.001
mitochondrial ribosomal protein L18 / Mrpl18 / XM_214751 / 1.30 / 0.001
mitochondrial ribosomal protein L50 / Mrpl50 / XM_342835 / 1.30 / <0.001
mitochondrial ribosomal protein L51 / Mrpl51 / XM_216269 / 1.29 / <0.001
mitochondrial ribosomal protein L53 / Mrpl53 / XM_342712 / 1.28 / 0.005
mitochondrial ribosomal protein L32 / Mrpl32 / XM_214491 / 1.27 / <0.001
mitochondrial ribosomal protein L2 / Mrpl2 / XM_217355 / 1.27 / <0.001
mitochondrial ribosomal protein S18A / Mrps18a / NM_198756 / 1.27 / <0.001
mitochondrial ribosomal protein S23 / Mrps23 / XM_340874 / 1.27 / <0.001
mitochondrial ribosomal protein L48 / Mrpl48 / XM_215009 / 1.27 / 0.001
mitochondrial ribosomal protein L55 / Mrpl55 / XM_213321 / 1.26 / 0.001
mitochondrial ribosomal protein L1 / Mrpl1 / XM_214008 / 1.25 / 0.001
mitochondrial ribosomal protein L16 / Mrpl16 / NM_001009647 / 1.25 / <0.001
mitochondrial ribosomal protein L44 / Mrpl44 / XM_217450 / 1.24 / 0.002
mitochondrial ribosomal protein S12 / Mrps1 / XM_214890 / 1.23 / <0.001